Operation Rocket
by Lennybobenny
Summary: An ordinary boy destined for greatness sets out on a journey full of deception and twists. After the death of his father figure, Professor Elm, the boy discovers an incredible power that only he possesses. A little bit of romance/love interest too.
1. He Has Returned

**Chapter One: He Has Returned**

It was a cold night in New Bark Town. The few houses in the small town were a fair distance apart. The architecture was modern, brick and wooden walls along with a smooth wooden roof. A small garden was being grown. The flowers were close together, each a different color and scent, sending a fresh aroma throughout the town.

But nobody could have predicted what happened that night.

"Coast is clear, boss."

A group of seven men dressed in full black suits, along with a black ski mask over their faces, crept into the small town. Each of them had a few PokeBalls strapped around their waste, along with a gun and some extra ammunition.

They walked up to Professor Elm's laboratory, which had some of the most advanced technology known to the Pokemon world. The group's boss, who could be identified by his unique badge on his clothing, ducked and pulled out two clips to pick the lock.

The boss took out a small machine with a wire and connected it to the lab's security system, which hacked the security code and turned off the security. "Security is down. Stay quiet and find the three rare Pokemon. Once we have those, mission is over."

The lab was filled with light coming from the machines, but the main light on the ceiling was turned off. In the corner of the room was a small healing machine, with 6 PokeBall slots. Four shelves with glass windows stood. Inside sat different documents and accessories.

One of the men found a machine that looked like no other machine in the lab. "Boss, I found something," he whispered.

His boss and the rest of the team walked over to him. The machine had a big, red light on top of it. On the front if it was a hand recognition system to open what was inside it.

"Don't touch the machine. I'm going to get Professor Elm's hand," the boss said. "All of you stay here." The boss pulled out his pistol and attached a silencer to it. He walked out of the lab without closing the door to minimize the amount of noise he made and walked up the stairs to the Professor's house. He picked the lock and quietly entered the house.

The kitchen was to his left as he walked in, with a basic fridge, stove, and sink along with a blue counter surrounding them. To his right was the living room, with a large TV, two couches, a table, and a bookshelf.

He continued down the hall of the house and pointed his gun to the door of the bedroom. He slowly turned the knob and sneaked inside the room.

The professor and his wife slept in the bed, side-by-side. Her head was snuggled under his arm like a baby. _I hate this kind of work. _He pointed the pistol at Elm's head and shot. Despite the suppressor the sound of a firing gun woke up his wife, so he shot her too.

He pulled out a knife from his waist belt and cut the professor's arm off. Without wasting any time, he walked out of the room. As he walked by Elm's son's room, he noticed it was slightly open. _I could have sworn that the room was closed. _He stopped thinking and headed back to the laboratory.

Elm's son peered through the slightly opened door as his family's murderer exited his house. He rushed to his parents' room and saw their bodies, motionless. The bed was soaked with blood, shocking the boy into unconsciousness.

The boss returned to the lab and put the hand on the hand recognition system. The machine opened, revealing three PokeBalls. "Good work, team," the boss complimented. Chuckling darkly, he put the three PokeBalls on his waist belt and fled the town with his team.

* * *

><p>Jimmy awoke to the screams of several town residents at six in the morning. He sprang out of bed without changing into any regular clothing.<p>

His room was clean, not like most people his age. The TV was on the edge of his room covered in dust, along with his Wii game system. His laptop sat on his table which he did most of his schoolwork on.

He had a black T-shirt on and gold-colored shorts. His blue eyes were as clear as the sky, but his unusual hairstyle sometimes went over his face, covering his eyes. His hair was a natural black with a tuft that stuck out.

He grabbed his hat and ran down the stairs, but his mom wasn't there. "Looks like she woke up too," he said to himself. The fridge was wide open, so Jimmy jumped over his counter and grabbed an apple and took a bite. With the apple in his right hand, he ran outside to see what all the commotion was about.

Several officers parked their motorcycles and cars in front of the professor's lab and home. An ambulance was also parked, but much closer to the entrance of the house. Two men put a body-bag in the back of the ambulance and a few seconds later, two other men came down the stairs with a new body-bag.

"Jimmy!" his mom cried out. She ran up to him and hugged him. "You won't believe what happened," she said and wiped tears off her face.

"What happened here?" Jimmy asked.

She breathed in and stopped crying. "Professor Elm and his wife were murdered during the night. His son," she paused, her eyes growing watery again. "After their son woke up from being unconscious, he called the police which arrived here in a few minutes."

Jimmy's eyes widened. "But…but Elm was like a father to me."

"I know it's hard. His and his wife's funeral will be in the route past Cherrygrove. They'll be buried next to Mr. Pokemon's house."

"I'm guessing school is canceled?" Jimmy joked, even though it was uncalled for.

"Stay strong, champ," his mom said and patted him on the back.

Jimmy threw his apple on the ground, splattering into different pieces. He couldn't control the anger that raged inside of him. Because it was too early to see any real Pokemon battles to relieve his anger and stress, he decided to find a different way to see a battle.

He took out his PokeGear and dialed someone's number. "Hey Neordan, it's me Jimmy. I'm coming down for a few."

"Hey no problem. It's Tyrogue vs. a Hitmonlee down here. Money on who?"

"Twenty bucks on the Tyrogue. Those things are fighters," Jimmy joked.

Jimmy made his way to Cherrygrove City, which had a Pokemon Center and Mart. It's where most new trainers stopped to get some items before leaving on their Pokemon journey. Jimmy had always dreamed of becoming a trainer and venturing the world, but he lacked the skills and the money.

He walked into one of the old, worn out houses and went down the stairs to the basement.

Many people crowded around a big ring, with two Pokemon inside it. One was a beat-up Tyrogue from earlier in the battle and the other was a Hitmonlee without a scratch on it.

"Hey, Jimmy!" Neordan said. He had long, red hair and wore a black and red jacket with white pants. "Your Tyrogue isn't holding up. Hand over the twenty."

All the pent up anger inside him soon turned to pity as he saw the bedraggled and bloody Tyrogue in the corner of the ring. "Wait a second," Jimmy said. "Look at how beat up Tyrogue is. You're supposed to take them out of the ring at this stage."

"It's not up to me, Jimmy. The people want a fight."

"Not if I have anything to say," Jimmy said and jumped into the ring. "Come on, Tyrogue. I'm taking you to a Pokemon Center." He grabbed the Tyrogue and ran out of the ring.

"Hey, where do you think you're going?" said one of the thugs. "I put my money on that little guy!"

Jimmy sprinted up the stairs and headed to the Pokemon Center. He looked back to see if he had been followed, but it seems like they didn't care enough. "Please, heal this Pokemon. He's all beat up."

"Don't worry, with these new machines we can heal Pokemon instantly, even if they were in the worst condition," she said and took Tyrogue. She put him in a PokeBall and placed him on a machine on the counter. The PokeBall glowed for a few seconds and then stopped. The Nurse took the PokeBall off the machine and released Tyrogue. "Good as new in seconds!"

"You all right, little Tyrogue?" Jimmy asked. He had never met the Pokemon in his life, but he felt a connection between them. "Good as new." He chuckled and looked down at the Tyrogue.

Tyrogue jumped on Jimmy, hugged him, and began to shine brightly. When the brightness stopped, Tyrogue was gone.

"What in the world?"

The thug and a few of his thug friends bashed through the doors of the Pokemon Center. "Hey man, I believe you've got something we want."

"Looks guys, the Tyrogue literally just disappeared," Jimmy responded. "I have no idea where he went."

"Then I guess you're going to take the beating he was supposed to get." The thug walked up to Jimmy and cracked his knuckles. "Are you ready?"

_Come on Tyrogue!_

The thug threw a punch at him, but Jimmy moved his head and pushed the thug's hand to the side. Jimmy side-kicked him in the face and the thug fell back onto some plants.

"I guess I underestimated you," the thug said as he got back up. He wiped the blood off his lip and charged at Jimmy, but Jimmy moved to the side right as he was about to get hit and pushed the thug forward with a kick, stopping his momentum and smacking him into the counter.

_What just happened?_

The rest of the thugs ran out of the Pokemon Center, afraid of getting the same beating as their friend.

"Good work, trainer!" the Nurse exclaimed. "More people should be as brave as you. I'm calling the police right now!"

Jimmy sat down on one of the seats, still unclear of what happened. _Where'd you go, Tyrogue? And how did I beat up that thug?_

A male officer entered the Pokemon Center and arrested the thug. "May I ask what happened here?"

"Well, the thug came in talking about some Pokemon that I saved from a beating," Jimmy stopped before continuing. _He'll think I'm crazy if I tell him the Pokemon disappeared…_"And so he tried to fight for it back and attacked me, but I fought back and defeated him. By the time I looked to see where the Tyrogue was, well, it was gone."

"Can I see the surveillance footage please? It just seems a little farfetched, no offence."

"None taken."

The Nurse led the officer to the surveillance room and he saw that Tyrogue disappeared after a bright flash of light. "He has returned."

The officer ran back to the main room of the Pokemon Center and dialed a number on his PokeGear. "Sir, tell the Johto Security Agency that he has returned!"

Jimmy overheard the conversation, but didn't pay much attention. He was deep in thought. The memories of Tyrogue played in his head, as if he was there. As if he was the Tyrogue.

A JSA agent dressed in black walked into the Pokemon Center. "What are you talking about? This is not him!"

"Look at the footage! If it's not him, then it's another one!" the officer said, leading the agent into the surveillance room where he saw the bright flash.

"I can't believe it. After three years, we've found another one to complete the mission!" the agent exclaimed.

"Come with me, Jimmy," the agent said. "We have a lot to talk about."

The agent escorted Jimmy to the car. Jimmy had seen a JSA agent who had saved several people before, so he trusted the JSA. He believed it had something to do with what happened earlier, so he got in the car.

"We're going to take you to a high-level government facility. Trust me, everything will be explained," the agent said.

* * *

><p>The agent opened the door for Jimmy and led him to the house that they had parked next to. It was a small house in Ecruteak City and was in the style of all the houses in that city: wooden walls, wooden roof, wooden everything.<p>

One man was in the room, sitting on the floor and meditating. "Did you bring the boy with you, Agent Oak?" he asked, but his voice was weak.

"Yes Grandpa, he's here," the agent responded. "Sorry for how mysterious things happened earlier. My name is Agent Gary Oak, member of the Johto and Kanto Security Agency, but currently I'm stationed in Johto."

"And who is he?" Jimmy asked.

"That's my Grandpa. You probably know him as Professor Oak."

"No way! THE Professor Oak?" Jimmy asked. He was a big fan of him ever since Professor Elm told him the great stories when Elm was under Oak's teaching.

"Yes, it's me. But I need you to be serious now," Professor Oak said and stood up. "The ability you possess is powerful and I see that you have merged with your first Pokemon already."

"Merged? You mean…me and that Tyrogue…we're the same person?" Jimmy exclaimed.

"Actually, that Tyrogue is now part of your memory. Everything the Tyrogue was and what it can do is locked in your memory."

"Is that how I was able to beat up the thug?"

"Precisely. You triggered Tyrogue's skills by thinking of Tyrogue. You had a surge of energy and were able to use his skills. But this surge of energy is only temporary and it cannot be used constantly, or else you might kill yourself in the process."

"So, could I merge with other Pokemon if I wanted to?"

"It's not that simple," Gary interjected. "You saved the Tyrogue, which created a special bond between the two of you. This special bond allowed you to merge with it and a bond is always needed for a merge."

"Are you guys just here to explain it to me? Or is there a greater purpose to this meeting?" Jimmy asked impatiently.

"You Soul Mergers are all the same," Oak chuckled. "The reason you are here is because your services are needed. You are going to become a JSA agent and work on a secret operation built on defeating Team Rocket."

"Is Team Rocket by any chance connected to the murder of Professor Elm?" Jimmy asked.

"Yes, the footage showed that trained Rocket agents did this, but fortunately not trained enough," Gary said. "One of them wasn't wearing gloves and we got a fingerprint, which identified one of their agents."

"So did you guys interrogate him or what? I'm not familiar with the drill."

"We haven't captured him yet. And that's where you come in," Oak said. "He's here in Ecruteak City. We took you to this JSA base for a reason. I'd honestly prefer taking you to my hometown in Kanto to brief you, but our Rocket agent and his friends are in the Burnt Tower as we speak. And your first mission awaits."

"So let me get this straight: I have the ability to merge with Pokemon, use superhuman skills, and am an official member of the JSA?"

"That's correct," Oak said.

"Great, let's get to my first mission."

* * *

><p><strong>Thank you very much for taking the time to read this first chapter! I'm a few chapters ahead (currently working on Chapter 4) so I'll post the next chapter soon, when I've got through most of Chapter 4 at least.<strong>

**All comments are appreciated, even if the criticism is extremely constructive. I've got big plans for the climax of the story. It has played over and over in my head so many times, so I would like at least a small amount of reviews to know someone is following along with my epic adventure.**


	2. Traitor

**I hope someone out there is reading this. If you are, please don't hesitate to review and speak your mind. All constructive criticism is welcomed. Without further ado, here is Chapter Two!**

* * *

><p><strong>Chapter Two: Traitor<strong>

Jimmy looked up at the Burnt Tower. It was the largest building in the Johto region, but nobody was ever brave enough to climb to the top of it.

Many myths are told about the tower's history; how there was a disastrous fire and the legendary Pokemon saved it from being destroyed.

The stairs leading towards the Burnt Tower had been made with new wood, but the tower itself was named a historical landmark. Nobody was allowed polish it in any way to keep the history for centuries to come.

He walked up the stairs to the tower. The door creaked open as he entered the room.

There were countless holes on the floor that when looked into only led to darkness. The sounds of wild Zubats and Koffings echoed throughout the first floor, but none approached Jimmy.

"Hey Gary, I'm in," Jimmy whispered into his PokeGear.

"They wouldn't be stupid enough to discuss their plans on the first floor," Gary said. "They probably went downstairs. It's said that ghosts live there, so nobody would go there and spy on them."

"I'm turning my PokeGear off. Don't want to make unneeded noise," Jimmy said and pressed a red button on his PokeGear.

He put it back on his waist belt and searched the room. The first level was where tourists went to see the fire's effect on the tower and the Pokemon living there.

At the edge of the first level was a hole, with a ladder sticking out of it. "Looks like I found my way down." He approached the hole and looked through it before going down. It was too dark to see anything, but a crying sound echoed through the underground level.

Jimmy silently went down the ladder and took out his flashlight. He set it on the lowest brightness level to attract the least amount of attention.

He followed down a narrow hallway, but could barely see anything. The crying got louder as he walked and the hallway became brighter, as if another light source was being used at the end of it.

Jimmy turned a corner and noticed three Rocket grunts and two dark figures. Through the shadows Jimmy couldn't identify them clearly, but he could see they weren't wearing Rocket uniforms.

"It seems like the Legendary Pokemon are deeper underground than we had first calculated," a Rocket grunt said.

"First you said they were going to be on the first floor, then the underground level, now you want us to go deeper?" a shadowy figure exclaimed loudly.

"Please Morty, we can't go back with failure. Giovanni will scold us," the other shadow figure responded.

_Morty? The Gym Leader?_

"Alright Eisune, tell the Geodude to dig deeper," Morty said. "I'll contact the other Gym Leaders in Team Rocket."

Jimmy's PokeGear got loose from his waist belt and fell on the floor, creating a loud 'dink' sound. "Crud."

"Hey, who's there?" a Rocket grunt asked and walked towards the corner. The Rocket grunt looked around, but couldn't see anyone.

Jimmy jumped from around the corner and punched the grunt in the face. The grunt nearly tripped on himself, but regained his balance.

"You have no idea who you're messing with, kid," the grunt said and pulled out his pistol. "What are you doing here?"

"Take care of the kid and the Legendary Beasts, Eisune. This isn't my problem anymore," Morty said. He walked past Jimmy and exited the underground level.

"Nobody is here to save you, so why don't you tell us why you're here?" Eisune asked.

"Well, here goes nothing," Jimmy said. _Let's do this, Tyrogue_. A surge of energy pulsed through his brain, playing memories of Tyrogue training in Cherrygrove City against wild Pokemon.

Jimmy grabbed the grunt's hand and twisted it, forcing him to drop the gun. He kicked the grunt in the chest and pushed him into another grunt. "Who's next?"

The last grunt tried to reach for his gun, but Jimmy jabbed him in the face and side-kicked him in the chest, pushing him against the wall.

"I'm always up for a good fight," Eisune chuckled. He cracked his knuckles and got into a fighting stance, one fist up and the other on the side of his hip.

Eisune jabbed with his front fist, but Jimmy blocked it and kneed him in the chest. While Eisune was regaining his balance, Jimmy reached for the gun that the grunt had dropped and pointed it at Eisune. "I wouldn't suggest you make another move." Jimmy picked up his PokeGear that he had dropped and called Gary. "I've got the bad guys. One escaped, but I identified him. We should be able to get him too."

In seconds, Gary and a trained team of agents entered the underground level.

"Eisune, so good to see you again," Gary said as he hand-cuffed him.

"Your new agent here is good," Eisune said with a small chuckle of defeat.

Jimmy crouched down and looked at the Geodude. "You can stop digging," Jimmy said, hoping the Pokemon would understand.

The Rock Pokemon stopped digging and climbed back up the hole he had dug. He smiled and opened up one of his fists.

"A high five?" Jimmy asked. He slapped his hand down on Geodude, and with a bright flash, Geodude was gone. "I don't understand. I just saved him. Doesn't he want to be free with the other Pokemon in the world?"

"We'll talk about this later, not with Rocket grunts in the room," Gary said.

* * *

><p>Gary locked the prisoners in the underground prison of the Ecruteak JSA base and rejoined with Jimmy on the first floor.<p>

"Mind giving me an explanation now?" Jimmy asked, growing impatient.

"Like I told you before, the Pokemon is repaying you by giving you his powers. The Geodude is still alive, but inside of you. The more you use the powers he gave you, the more powerful Geodude will become inside of you."

"I sort of get it," Jimmy said. "What are we going to do about Morty? He left before I fought the Rocket grunts and he also mentioned something about other Gym Leaders being involved in Team Rocket."

"Already ahead of you," Gary smirked. "One of the professor's stolen Pokemon was being held by the Rocket grunt. It's a Cyndaquil." He pressed the middle button on the PokeBall and a red beam of light transformed into the fire Pokemon. A small flame sat on its back. When the flame was small, the Pokemon was calm and collected, but when the flame grew, it meant it was angry or battle-ready.

"Wow? Does it have any clues or something?" Jimmy asked.

"No," Gary said and chuckled, amused by Jimmy's lack of understanding. "You're going to challenge Morty to a 1-on-1 Gym Battle."

"But I hardly know the Pokemon!"

"Then here's your chance to befriend it. Every agent needs a partner Pokemon. Mine is Blastoise. Yours will be Cyndaquil. Try not to merge with it," Gary joked and patted Jimmy on the back. "You better get going before Morty realizes his team was captured." Gary threw Jimmy the PokeBall for Cyndaquil. "Take good care of him."

Jimmy pointed the PokeBall at Cyndaquil and put him back in it. "Come on, little buddy."

* * *

><p>Jimmy walked through the doors to the gym, but it was almost pitch-black. "Light the way," Jimmy said and let Cyndaquil out of his PokeBall.<p>

Cyndaquil's flame grew on his back, nearly lighting up the whole room.

Morty looked up to see his challenger, but his hopeful expression turned into an angered one. His blonde hair reached down to his shoulders and his blue headband was wrapped tightly around his head. "Are you here to arrest me?"

"I'm here to battle you, Morty. How about I make you a deal?" Jimmy asked. "I beat you in a Pokemon battle and you tell me who the other Rocket Gym Leaders are. You'll also be arrested."

"What's in it for me if I beat you?"

"You'll walk. We won't arrest you or question you. Take my word for it." Cyndaquil walked up in front of Jimmy and the flame on its back grew even larger.

"Quite a big flame you're racking up there," Morty said. "Think it can take on my Haunter?" He threw his PokeBall into the air and released his ghostly Pokemon.

Haunter's dark face lit up by the flame's light and his tongue stuck out. Its two claw arms floated next to his body, but weren't connected to it.

"Scared yet?" Morty smirked. "Haunter, use Lick!" Morty commanded.

Without Jimmy's command, Cyndaquil jumped over Haunter as it rushed at him and shot a series of flames out of his mouth.

"Now I see why Rocket wanted this Cyndaquil so bad," Jimmy said.

Smoke filled the room as the flames collided with the ghost Pokemon, but Haunter shook it off.

"Haunter, use Shadow Ball!" Haunter's arms came closer together and a dark blob formed in between his hands. Haunter released the shadow attack at Cyndaquil, but Cyndaquil retaliated with his own Flamethrower attack.

The two attacks collided, sending a small shockwave through the battlefield. Cyndaquil's Flamethrower seemed to be pushing the Shadow Ball back to Haunter, but the Shadow Ball also became stronger and pushed the Flamethrower back.

The power struggle ended as Cyndaquil released all of his remaining strength into the attack. The Shadow Ball flew back at Haunter, followed by the powerful Flamethrower attack. The collision between Haunter and the powerful attacks caused a massive explosion.

Smoke covered the battlefield, causing both trainers to cough. As it slowly settled, Cyndaquil's flame became visible. Haunter was on the ground, defeated and knocked out.

"You're under arrest, Morty."

"No, it can't end like this!" Morty screamed. He pulled out a pistol and aimed it at Jimmy. "Give me one good reason not to pull the trigger!"

_Geodude!_

A surge pulsed through his brain, similar to that of Tyrogue. Images and memories of Geodude throwing rocks at wild Pokemon played through his head.

"I can't give you a reason," Jimmy said.

Morty pulled the trigger and the bullet rushed towards Jimmy. In that split second, Jimmy raised a wall of stone from the ground and blocked the bullet. He moved his hands forward and the wall of stone rushed towards Morty and smacked into him. He flew backwards and hit the wall at the back of the gym.

Jimmy ran up to Morty and grabbed him by his collar. "Who are the other Gym Leaders?"

Morty tried to headbutt Jimmy, but Jimmy's skin was as hard as rock. "Ok! Ok! Ok I'll tell you!" Morty screamed in pain. "Clair and Chuck are both Rocket operatives."

"Thanks," Jimmy said and punched Morty in the face, knocking him out. He pulled out his PokeGear and dialed Gary's number. "Hey Gary, bag and tag him. I got the intel we needed."

* * *

><p>"Good work, Jimmy," Gary said. "You're officially a member of this operation, which means that you get your very own alias."<p>

"You mean like in the movies?" Jimmy joked.

"You need to take this seriously. You are now called Agent Gold. We don't want Team Rocket to find out our agents' real names. I already made that mistake before," Gary explained. "And from now on, you will call me Agent Blue. Understood?"

"Yeah, gotcha. What do we do about Clair and Chuck? They seem dangerous."

"Don't worry, we'll make a plan on how to get them tomorrow. Right now, what you need is a good night's rest."

Before leaving the room, Jimmy took one last look at Cyndaquil's PokeBall.

"Professor Elm would have wanted you to have that Cyndaquil," Gary said.

"I just can't believe he's gone. He taught me everything I know. How to tie my shoes, how to properly eat, and even how to cook scrambled eggs," Jimmy said. "He was truly like a father to me…"

"Don't trouble yourself with these thoughts. We'll find who did this to the professor, I promise," Professor Oak said as he walked into the Ecruteak JSA base. "I heard the way that man talked about you. He believed you had so much potential and he was right. He just didn't know what kind of potential you possessed."

"Grandpa is right. We'll find him," Gary said. "And when we do, that person will be locked up forever."

"Thanks guys," Jimmy said. "Where are we going tomorrow?"

"We don't have the plan yet. A new agent will be joining our team tomorrow and will help us come up with something. I know you're still new to the way things work, but try not to break under the pressure so quickly. We don't want you ending up like the other Soul Merger."

"Gotcha," Jimmy said and went to his room.

"This whole operation rests on that boy's shoulders," Professor Oak said. "Train him well. He'll need it for what's to come."

* * *

><p>"Boss, our team was captured, along with Morty and Elm's Pokemon," a Rocket grunt spoke into a phone.<p>

"Do we know who is responsible for this?"

"It's Agent Blue and his team. What do you want me to do?"

"Giovanni wants Blue alive and that's what he's going to get," Boss replied and chuckled darkly. "He won't even know what's coming."

* * *

><p><strong>And that was Chapter Two for you. If you liked it, remember to say something. If you didn't, well, that's a shame and I would also like to know why you didn't like it. I have big plans in terms of plot and character development, so if any of you are tuned in, you can look forward to some big steps up for plot. <strong>


End file.
